Robust precoding is efficiently feasible in frequency division duplex (FDD) systems by incorporating the learnt statistics of the propagation environment through a generative model. We build on previous work that successfully designed site-specific precoders based on a combination of Gaussian mixture models (GMMs) and graph neural networks (GNNs). In this paper, by utilizing a vector quantized-variational autoencoder (VQ-VAE), we circumvent one of the key drawbacks of GMMs, i.e., the number of GMM components scales exponentially to the feedback bits. In addition, the deep learning architecture of the VQ-VAE allows us to jointly train the GNN together with VQ-VAE along with pilot optimization forming an end-to-end (E2E) model, resulting in considerable performance gains in sum rate for multi-user wireless systems. Simulations demonstrate the superiority of the proposed frameworks over the conventional methods involving the sub-discrete Fourier transform (DFT) pilot matrix and iterative precoder algorithms enabling the deployment of systems characterized by fewer pilots or feedback bits.